期刊
NATURE PROTOCOLS
卷 3, 期 6, 页码 977-990出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/nprot.2008.62
关键词
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资金
- European Union [FP6-502828, UE-512092]
- US National Institutes of Health [HL740472]
- Spanish Comision Interministerial de Ciencia y Tecnologia [BFU2004-00217]
- Spanish Ministerio de Educacion y Ciencias [CSD2006-0023, BIO2007-67150-C03-01 and -03]
- Spanish Fondo de Investigacion Sanitaria [04/0683]
- Comunidad de Madrid [S-GEN-0166-2006]
- NATIONAL HEART, LUNG, AND BLOOD INSTITUTE [R01HL070472] Funding Source: NIH RePORTER
We describe a collection of standardized image processing protocols for electron microscopy single-particle analysis using the XMIPP software package. These protocols allow performing the entire processing workflow starting from digitized micrographs up to the final refinement and evaluation of 3D models. A particular emphasis has been placed on the treatment of structurally heterogeneous data through maximum-likelihood refinements and self-organizing maps as well as the generation of initial 3D models for such data sets through random conical tilt reconstruction methods. All protocols presented have been implemented as stand-alone, executable python scripts, for which a dedicated graphical user interface has been developed. Thereby, they may provide novice users with a convenient tool to quickly obtain useful results with minimum efforts in learning about the details of this comprehensive package. Examples of applications are presented for a negative stain random conical tilt data set on the hexameric helicase G40P and for a structurally heterogeneous data set on 70S Escherichia coli ribosomes embedded in vitrified ice.
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